Skull, the evil leader of the terrorist organization known as Black Ghost, has nine powerful cyborgs under his control. But Dr. Isaac Gilmore, the Black Ghosts cybernetics scientist, decides to go rogue, helping the cyborgs turn against Skull and his evil organization. Black Ghost wishes to start the next major world war by flooding the market with weapons of mass destruction. It seems the nine brave cyborgs have their work cut out for them, as Black Ghost is determined to bring those nine cyborgs down.

In an attempt to gather information on immortality, scientists from around the world have assembled to study "Heaven's Gate"—the tomb turned laboratory of the mythical king Gilgamesh. But soon enough, the research is deemed unethical and all planned work comes to a halt. However, a group of terrorists pay this no thought and storm into Heaven's Gate, ultimately causing an explosion that leads to the collapse of the advanced information civilization. Many years after the incident, the siblings Tatsuya and Kiyoko Madoka are on the run from thugs. Yet this seems to be the least of their worries as they find themselves in the midst of a war between two powerful cryptic factions. With both groups claiming to fight for the betterment of society, Tatsuya and Kiyoko will have to find a way to decide who to trust.